I installed 3.1.2 and it caused the secure pages to be displayed without the header image, background image, and some of the theme color options. I'm using the Vende theme with Woocommerce. I was in a big hurry so I installed version 3.0.4 which seems to work just fine. I thought you would like to know. Sorry I couldn't keep it around so you could troubleshoot.

At this moment where is no background image in all my pages except secured.
I use most current version of plugin and WP and i can not downgrade because of compability problems with qTranslate in older versions of plugin.